Opposition lawmakers surged toward the chairman's seat as they realized something was up after ruling party legislators had gathered at the podium to protect him.
As the scrum intensified, ruling party lawmakers still in their seats stood up to signal their support for the legislation, though there didn't appear to be an audible announcement of what they were voting on.
The legislative standoff is the latest development in a yearslong national debate about the way Japan uses its military, a central question for the country since its armed forces were defeated in World War II seven decades ago.
A senior opposition member later said his party would not accept the vote because the ruling bloc had cheated.
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"You saw the scene. We do not recognize there was a vote. How can you tell what happened, what the chairman was calling?" said Tetsuro Fukuyama, committee leader for the Democratic Party of Japan.
If the vote stands, the legislation will go to the upper house of parliament for final approval. The bills were passed by the more powerful lower house in July.
"We are relieved. Now we will do our utmost for approval of the bills in a house vote."
The ruling party's ploy ended nearly 24 hours of delaying tactics by the opposition, which plans more when the full upper house takes up the bills.
Before the vote, opposition lawmakers had introduced a no-confidence motion against the committee chairman, who earlier had tried to force the meeting to start.
The legislation would allow the military to defend Japan's allies even when the country isn't under attack, work more closely with the US and other allies, and do more in international peacekeeping.